TNRC18

protein-coding

trinucleotide repeat containing 18

Gene summary

Enables histone H3K9me2/3 reader activity. Involved in protein localization to chromatin and transposable element silencing by heterochromatin formation. Located in cytosol; mitochondrion; and nucleus. Is active in chromatin and nucleus. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001080495.3

Inheritance

—

ClinVar variants

U:744B:117

Top phenotype

TNRC18-related disorder

gnomAD constraint

pLI —, LoF o/e 0.19

Max pathogenic AF

—

Genomic locus

chr7:5,306,790-5,425,414

External References & Databases

Ensembl (ENSG00000182095)

Transcript & Mutation Effects

hg38 • Region Span ~118.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TNRC18 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 746

not providedTotal: 118

TNRC18-related disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001080495.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			8 clinvar	51 clinvar	23 clinvar	82
missense			722 clinvar	31 clinvar	12 clinvar	765
nonsense			3 clinvar			3
start loss						0
frameshift			6 clinvar			6
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	744	82	35	861

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 28 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001080495.3	RefSeq	NP_001073964.2	29	MANE Select
ENST00000430969.6	Ensembl	ENSP00000395538.1	29	MANE Select
ENST00000328270.3	Ensembl	ENSP00000329902.3	5	Standard
ENST00000399434.2	Ensembl	ENSP00000382364.2	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

chromatin binding

Cellular Component

nucleus
nucleoplasm
mitochondrion
cytosol
nuclear membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000430969
Coding exons: 29
Length: 118625
Individuals with no LoFs: 124619
Homozygous LoFs: 0
Heterozygous LoFs: 12
Defined: 124631
p: 0.0000481

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.262	1647	1.62e+3	1.02	0.000114	18328
Missense (PolyPhen)		404	388.84	1.039		4619
Synonymous	-7.12	1004	755	1.33	0.0000611	6321
Loss of Function	6.91	16	84.6	0.189	0.00000404	1148

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000087	0.000065	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.000056	0.000056	rare
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.000069	0.000062	rare
South Asian	0	0.0	absent
Other	0.00017	0.00017	rare

dbNSFP Gene Annotations

Source: dbNSFP

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: E
Indispensability score: 0.606

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High